It has been a number of years since I have done anything of significance in C, so some best practices may have changed, but from a quick glance, I see a couple of things:

If you are looping through a list of items for, say, a 0-based copy, you may get better results from something like:
for (j=maxval; j; j--) {...}

The main function is a bit long for my tastes, although I understand that you are trying to do this for performance, so removing the function calls might make sense.

Some of the repeated board manipulations or constants should probably be put into macros. The loop for copying the board is used at least twice and could be macro-ized, and many of the constants are just magic numbers as I read through.

I agree. It grew over time. I am also more verbose than I need to be. I am using -O3 for gcc which I believe inlines whatever it can. I am potentially considering a new direction entirely so if I touch it again, I will certainly make more use of functions.

Some of the repeated board manipulations or constants should probably be put into macros

Macros are incredibly powerful but if you don't code enough in C to make them second nature they can have the opposite effect as intended (making code harder to understand rather than easier). I prefer to explicitly say what I am doing when working in a language I am not comfortable in so that I understand the code when I come back to it later. As far as magic numbers - yeah. I started to make variables to give them meaning but wasn't consistent as I tried to finish the code. In a re-write I would probably have some global static variables defined outside of main.

Other than that, do you have a profiler that shows any hotspots?

No. I was expecting someone to look at the way I copy one array to another and say a far more efficent way of doing that was memcopy with a working example but alas, no such luck.